Thanks for the detail, I decided that I will just update the v5 with the new engine details. I called the dvla to explain that I need to update the v5 with details of an engine and gearbox change (as it's an auto donor). They said just to update section 7 with engine number and include a cover letter stating transmission changed to manual.
I can also provide evidence by way of either garage services invoice or independent inspection (the latter may be slightly difficult)
It takes approx 4 weeks.
Once all done I should receive an arp after IVA and I register with personalised plate at application.
Total Spent so far - £xxxxx
Last Purchase - Engine mounts, steering wheel, slave cylinder.